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Francis WR, Eitel M, Vargas S, Garcia-Escudero CA, Conci N, Deister F, Mah JL, Guiglielmoni N, Krebs S, Blum H, Leys SP, Wörheide G. The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230423. [PMID: 37351491 PMCID: PMC10282587 DOI: 10.1098/rsos.230423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO2), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.
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Affiliation(s)
- Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Catalina A. Garcia-Escudero
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Deister
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jasmine L. Mah
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Nadège Guiglielmoni
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sally P. Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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Nishi M, Kobayashi H, Amano T, Sakate Y, Bito T, Arima J, Shimizu K. Identification of the Domains Involved in Promotion of Silica Formation in Glassin, a Protein Occluded in Hexactinellid Sponge Biosilica, for Development of a Tag for Purification and Immobilization of Recombinant Proteins. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:739-747. [PMID: 32291549 DOI: 10.1007/s10126-020-09967-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Glassin, a protein occluded in biosilica of the hexactinellid sponge Euplectela, promotes silica formation from silicic acid at room temperature and neutral pH and is characterized by its primary structure which consists of a tandem repeat carrying three distinct domains, histidine and aspartic acid-rich (HD) domain, proline-rich (P) domain, and histidine and threonine-rich (HT) domain. The present study aims to clarify the domain responsible for the promotion of silica formation and to demonstrate usefulness of glassin and its domain as a tag for purification and immobilization of recombinant proteins. When each domain was mixed with silicic acid at neutral pH, silica was formed with HD domain as well as glassin, or a single repeat, but not with P or HT domain. Neither of amino or carboxy-terminal half of HD domain induced silica formation. The amount of silica formed with HD domain was significantly lower than that of glassin or a single repeat. HD domain fused with HT domain raised the amount of silica formed, while a HD domain fused with P domain, a mixture of HD and P domains, or a mixture of HD and HT domains has little effect on the promotion of silica formation. Collectively, a minimum sequence for promotion of silica formation is HD domain, whose activity can be enhanced by HT domain through a topological effect. In addition, practicality of glassin and HD domain was demonstrated by fusion of these sequences to green fluorescent protein which was successfully purified with Ni affinity chromatography and immobilized on silica.
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Affiliation(s)
- Michika Nishi
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Hiroki Kobayashi
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Taro Amano
- Division of Agricultural Science, Graduate studies of Sustainability Science, Tottori University Graduate School, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Yuto Sakate
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Tomohiro Bito
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Jiro Arima
- Department of Life Environmental Agriculture, Faculty of Agriculture, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8553, Japan
| | - Katsuhiko Shimizu
- Platform for Community-based Research and Education, Tottori University, 4-101, Koyama-cho Minami, Tottori, 680-8550, Japan.
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